feat: cornerstone3D stack and volume viewports (#2787)

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
2022-07-27 12:39:04 -04:00
1 parent 86dcaf6293
commit bd1c38c00c
@@ -1,4 +1,4 @@
-import React, { useCallback, useContext, useEffect } from 'react';
+import React, { useContext, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import { Machine } from 'xstate';
 import { useMachine } from '@xstate/react';
@@ -18,14 +18,14 @@ TrackedMeasurementsContext.displayName = 'TrackedMeasurementsContext';
 const useTrackedMeasurements = () => useContext(TrackedMeasurementsContext);

 const SR_SOPCLASSHANDLERID =
-  '@ohif/extension-dicom-sr.sopClassHandlerModule.dicom-sr';
+  '@ohif/extension-cornerstone-dicom-sr.sopClassHandlerModule.dicom-sr';

 /**
 *
 * @param {*} param0
 */
 function TrackedMeasurementsContextProvider(
-  { servicesManager, extensionManager }, // Bound by consumer
+  { servicesManager, commandsManager, extensionManager }, // Bound by consumer
  { children } // Component props
 ) {
  const [viewportGrid, viewportGridService] = useViewportGrid();
@@ -34,10 +34,8 @@ function TrackedMeasurementsContextProvider(
  const machineOptions = Object.assign({}, defaultOptions);
  machineOptions.actions = Object.assign({}, machineOptions.actions, {
    jumpToFirstMeasurementInActiveViewport: (ctx, evt) => {
-      const {
-        DisplaySetService,
-        MeasurementService,
-      } = servicesManager.services;
+      const { MeasurementService } = servicesManager.services;
+
      const { trackedStudy, trackedSeries } = ctx;
      const measurements = MeasurementService.getMeasurements();
      const trackedMeasurements = measurements.filter(
@@ -46,11 +44,11 @@ function TrackedMeasurementsContextProvider(
          trackedSeries.includes(m.referenceSeriesUID)
      );

-      const id = trackedMeasurements[0].id;
+      const uid = trackedMeasurements[0].uid;

      MeasurementService.jumpToMeasurement(
        viewportGrid.activeViewportIndex,
-        id
+        uid
      );
    },
    showStructuredReportDisplaySetInActiveViewport: (ctx, evt) => {
@@ -58,9 +56,9 @@ function TrackedMeasurementsContextProvider(
        const StructuredReportDisplaySetInstanceUID =
          evt.data.createdDisplaySetInstanceUIDs[0].displaySetInstanceUID;

-        viewportGridService.setDisplaysetForViewport({
+        viewportGridService.setDisplaySetsForViewport({
          viewportIndex: evt.data.viewportIndex,
-          displaySetInstanceUID: StructuredReportDisplaySetInstanceUID,
+          displaySetInstanceUIDs: [StructuredReportDisplaySetInstanceUID],
        });
      }
    },
@@ -73,16 +71,16 @@ function TrackedMeasurementsContextProvider(
      const measurementIds = filteredMeasurements.map(fm => fm.id);

      for (let i = 0; i < measurementIds.length; i++) {
-        MeasurementService.remove(measurementIds[i], 'app-source');
+        MeasurementService.remove(measurementIds[i]);
      }
    },
    clearAllMeasurements: (ctx, evt) => {
      const { MeasurementService } = servicesManager.services;
      const measurements = MeasurementService.getMeasurements();
-      const measurementIds = measurements.map(fm => fm.id);
+      const measurementIds = measurements.map(fm => fm.uid);

      for (let i = 0; i < measurementIds.length; i++) {
-        MeasurementService.remove(measurementIds[i], 'app-source');
+        MeasurementService.remove(measurementIds[i]);
      }
    },
  });
@@ -101,6 +99,7 @@ function TrackedMeasurementsContextProvider(
    }),
    promptSaveReport: promptSaveReport.bind(null, {
      servicesManager,
+      commandsManager,
      extensionManager,
    }),
    promptHydrateStructuredReport: promptHydrateStructuredReport.bind(null, {
@@ -134,13 +133,15 @@ function TrackedMeasurementsContextProvider(
    if (viewports.length > 0) {
      const activeViewport = viewports[activeViewportIndex];

-      if (!activeViewport || !activeViewport.displaySetInstanceUID) {
+      if (!activeViewport || !activeViewport?.displaySetInstanceUIDs?.length) {
        return;
      }

+      // Todo: Getting the first displaySetInstanceUID is wrong, but we don't have
+      // tracking fusion viewports yet. This should change when we do.
      const { DisplaySetService } = servicesManager.services;
      const displaySet = DisplaySetService.getDisplaySetByUID(
-        activeViewport.displaySetInstanceUID
+        activeViewport.displaySetInstanceUIDs[0]
      );

      // If this is an SR produced by our SR SOPClassHandler,
@@ -197,6 +198,7 @@ function TrackedMeasurementsContextProvider(
 TrackedMeasurementsContextProvider.propTypes = {
  children: PropTypes.oneOf([PropTypes.func, PropTypes.node]),
  servicesManager: PropTypes.object.isRequired,
+  commandsManager: PropTypes.object.isRequired,
  extensionManager: PropTypes.object.isRequired,
 };

@@ -1,12 +1,15 @@
-import cornerstoneTools from 'cornerstone-tools';
+import { utilities, metaData } from '@cornerstonejs/core';
 import OHIF, { DicomMetadataStore } from '@ohif/core';
 import getLabelFromDCMJSImportedToolData from './utils/getLabelFromDCMJSImportedToolData';
-import getCornerstoneToolStateToMeasurementSchema from './getCornerstoneToolStateToMeasurementSchema';
 import { adapters } from 'dcmjs';

 const { guid } = OHIF.utils;
-const globalImageIdSpecificToolStateManager =
-  cornerstoneTools.globalImageIdSpecificToolStateManager;
+const { MeasurementReport, CORNERSTONE_3D_TAG } = adapters.Cornerstone3D;
+
+const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
+const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
+
+const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];

 /**
 *
@@ -24,8 +27,8 @@ export default function _hydrateStructuredReport(

  // TODO -> We should define a strict versioning somewhere.
  const mappings = MeasurementService.getSourceMappings(
-    'CornerstoneTools',
-    '4'
+    CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+    CORNERSTONE_3D_TOOLS_SOURCE_VERSION
  );

  if (!mappings || !mappings.length) {
@@ -40,29 +43,38 @@ export default function _hydrateStructuredReport(
    displaySet.SOPInstanceUID
  );

-  const { MeasurementReport } = adapters.Cornerstone;
-
  const sopInstanceUIDToImageId = {};
+  let imageIdsForToolState = [];

  displaySet.measurements.forEach(measurement => {
    const { ReferencedSOPInstanceUID, imageId } = measurement;
+    imageIdsForToolState.push(imageId);
    if (!sopInstanceUIDToImageId[ReferencedSOPInstanceUID]) {
      sopInstanceUIDToImageId[ReferencedSOPInstanceUID] = imageId;
    }
  });

+  const datasetToUse = _mapLegacyDataSet(instance);
+
  // Use dcmjs to generate toolState.
-  const storedMeasurementByToolType = MeasurementReport.generateToolState(
-    instance
+  const storedMeasurementByAnnotationType = MeasurementReport.generateToolState(
+    datasetToUse,
+    // NOTE: we need to pass in the imageIds to dcmjs since the we use them
+    // for the imageToWorld transformation. The following assumes that the order
+    // that measurements were added to the display set are the same order as
+    // the measurementGroups in the instance.
+    sopInstanceUIDToImageId,
+    utilities.imageToWorldCoords,
+    metaData
  );

  // Filter what is found by DICOM SR to measurements we support.
-  const mappingDefinitions = mappings.map(m => m.definition);
+  const mappingDefinitions = mappings.map(m => m.annotationType);
  const hydratableMeasurementsInSR = {};

-  Object.keys(storedMeasurementByToolType).forEach(key => {
+  Object.keys(storedMeasurementByAnnotationType).forEach(key => {
    if (mappingDefinitions.includes(key)) {
-      hydratableMeasurementsInSR[key] = storedMeasurementByToolType[key];
+      hydratableMeasurementsInSR[key] = storedMeasurementByAnnotationType[key];
    }
  });

@@ -70,12 +82,13 @@ export default function _hydrateStructuredReport(
  const imageIds = [];

  // TODO: notification if no hydratable?
-  Object.keys(hydratableMeasurementsInSR).forEach(toolType => {
-    const toolDataForToolType = hydratableMeasurementsInSR[toolType];
+  Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
+    const toolDataForAnnotationType =
+      hydratableMeasurementsInSR[annotationType];

-    toolDataForToolType.forEach(data => {
+    toolDataForAnnotationType.forEach(toolData => {
      // Add the measurement to toolState
-      const imageId = sopInstanceUIDToImageId[data.sopInstanceUid];
+      const imageId = sopInstanceUIDToImageId[toolData.sopInstanceUid];

      if (!imageIds.includes(imageId)) {
        imageIds.push(imageId);
@@ -88,7 +101,7 @@ export default function _hydrateStructuredReport(

  for (let i = 0; i < imageIds.length; i++) {
    const imageId = imageIds[i];
-    const { SeriesInstanceUID, StudyInstanceUID } = cornerstone.metaData.get(
+    const { SeriesInstanceUID, StudyInstanceUID } = metaData.get(
      'instance',
      imageId
    );
@@ -106,43 +119,49 @@ export default function _hydrateStructuredReport(
    }
  }

-  Object.keys(hydratableMeasurementsInSR).forEach(toolType => {
-    const toolDataForToolType = hydratableMeasurementsInSR[toolType];
+  Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
+    const toolDataForAnnotationType =
+      hydratableMeasurementsInSR[annotationType];

-    toolDataForToolType.forEach(data => {
+    toolDataForAnnotationType.forEach(toolData => {
      // Add the measurement to toolState
-      const imageId = sopInstanceUIDToImageId[data.sopInstanceUid];
+      const imageId = sopInstanceUIDToImageId[toolData.sopInstanceUid];

-      data.id = guid();
+      toolData.uid = guid();

-      const instance = cornerstone.metaData.get('instance', imageId);
+      const instance = metaData.get('instance', imageId);
      const {
-        SOPInstanceUID,
        FrameOfReferenceUID,
-        SeriesInstanceUID,
-        StudyInstanceUID,
+        // SOPInstanceUID,
+        // SeriesInstanceUID,
+        // StudyInstanceUID,
      } = instance;

-      // Let the measurement service know we added to toolState
-      const toMeasurementSchema = getCornerstoneToolStateToMeasurementSchema(
-        toolType,
-        MeasurementService,
-        DisplaySetService,
-        SOPInstanceUID,
-        FrameOfReferenceUID,
-        SeriesInstanceUID,
-        StudyInstanceUID
+      const annotation = {
+        annotationUID: toolData.annotation.annotationUID,
+        data: toolData.annotation.data,
+        metadata: {
+          toolName: annotationType,
+          referencedImageId: imageId,
+          FrameOfReferenceUID,
+        },
+      };
+
+      const source = MeasurementService.getSource(
+        CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+        CORNERSTONE_3D_TOOLS_SOURCE_VERSION
      );
+      annotation.data.label = getLabelFromDCMJSImportedToolData(toolData);

-      const source = MeasurementService.getSource('CornerstoneTools', '4');
-
-      data.label = getLabelFromDCMJSImportedToolData(data);
+      const matchingMapping = mappings.find(
+        m => m.annotationType === annotationType
+      );

      MeasurementService.addRawMeasurement(
        source,
-        toolType,
-        data,
-        toMeasurementSchema,
+        annotationType,
+        { annotation },
+        matchingMapping.toMeasurementSchema,
        dataSource
      );

@@ -159,3 +178,66 @@ export default function _hydrateStructuredReport(
    SeriesInstanceUIDs,
  };
 }
+
+function _mapLegacyDataSet(dataset) {
+  const REPORT = 'Imaging Measurements';
+  const GROUP = 'Measurement Group';
+  const TRACKING_IDENTIFIER = 'Tracking Identifier';
+
+  // Identify the Imaging Measurements
+  const imagingMeasurementContent = toArray(dataset.ContentSequence).find(
+    codeMeaningEquals(REPORT)
+  );
+
+  // Retrieve the Measurements themselves
+  const measurementGroups = toArray(
+    imagingMeasurementContent.ContentSequence
+  ).filter(codeMeaningEquals(GROUP));
+
+  // For each of the supported measurement types, compute the measurement data
+  const measurementData = {};
+
+  const cornerstoneToolClasses =
+    MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
+
+  const registeredToolClasses = [];
+
+  Object.keys(cornerstoneToolClasses).forEach(key => {
+    registeredToolClasses.push(cornerstoneToolClasses[key]);
+    measurementData[key] = [];
+  });
+
+  measurementGroups.forEach((measurementGroup, index) => {
+    const measurementGroupContentSequence = toArray(
+      measurementGroup.ContentSequence
+    );
+
+    const TrackingIdentifierGroup = measurementGroupContentSequence.find(
+      contentItem =>
+        contentItem.ConceptNameCodeSequence.CodeMeaning === TRACKING_IDENTIFIER
+    );
+
+    const TrackingIdentifier = TrackingIdentifierGroup.TextValue;
+
+    let [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
+    if (supportedLegacyCornerstoneTags.includes(cornerstoneTag)) {
+      cornerstoneTag = CORNERSTONE_3D_TAG;
+    }
+
+    const mappedTrackingIdentifier = `${cornerstoneTag}:${toolName}`;
+
+    TrackingIdentifierGroup.TextValue = mappedTrackingIdentifier;
+  });
+
+  return dataset;
+}
+
+const toArray = function(x) {
+  return Array.isArray(x) ? x : [x];
+};
+
+const codeMeaningEquals = codeMeaningName => {
+  return contentItem => {
+    return contentItem.ConceptNameCodeSequence.CodeMeaning === codeMeaningName;
+  };
+};
@@ -1,283 +0,0 @@
-export default function getCornerstoneToolStateToMeasurementSchema(
-  toolType,
-  MeasurementService,
-  DisplaySetService,
-  SOPInstanceUID,
-  FrameOfReferenceUID,
-  SeriesInstanceUID,
-  StudyInstanceUID
-) {
-  const _getValueTypeFromToolType = toolType => {
-    const {
-      POLYLINE,
-      ELLIPSE,
-      POINT,
-      BIDIRECTIONAL,
-    } = MeasurementService.VALUE_TYPES;
-
-    // TODO -> I get why this was attemped, but its not nearly flexible enough.
-    // A single measurement may have an ellipse + a bidirectional measurement, for instances.
-    // You can't define a bidirectional tool as a single type..
-    // OHIF-230
-    const TOOL_TYPE_TO_VALUE_TYPE = {
-      Length: POLYLINE,
-      EllipticalRoi: ELLIPSE,
-      Bidirectional: BIDIRECTIONAL,
-      ArrowAnnotate: POINT,
-    };
-
-    return TOOL_TYPE_TO_VALUE_TYPE[toolType];
-  };
-
-  switch (toolType) {
-    case 'Length':
-      return measurementData =>
-        Length(
-          measurementData,
-          SOPInstanceUID,
-          FrameOfReferenceUID,
-          SeriesInstanceUID,
-          StudyInstanceUID,
-          DisplaySetService,
-          _getValueTypeFromToolType
-        );
-    case 'Bidirectional':
-      return measurementData =>
-        Bidirectional(
-          measurementData,
-          SOPInstanceUID,
-          FrameOfReferenceUID,
-          SeriesInstanceUID,
-          StudyInstanceUID,
-          DisplaySetService,
-          _getValueTypeFromToolType
-        );
-    case 'EllipticalRoi':
-      return measurementData =>
-        EllipticalRoi(
-          measurementData,
-          SOPInstanceUID,
-          FrameOfReferenceUID,
-          SeriesInstanceUID,
-          StudyInstanceUID,
-          DisplaySetService,
-          _getValueTypeFromToolType
-        );
-    case 'ArrowAnnotate':
-      return measurementData =>
-        ArrowAnnotate(
-          measurementData,
-          SOPInstanceUID,
-          FrameOfReferenceUID,
-          SeriesInstanceUID,
-          StudyInstanceUID,
-          DisplaySetService,
-          _getValueTypeFromToolType
-        );
-  }
-}
-
-function Length(
-  measurementData,
-  SOPInstanceUID,
-  FrameOfReferenceUID,
-  SeriesInstanceUID,
-  StudyInstanceUID,
-  DisplaySetService,
-  _getValueTypeFromToolType
-) {
-  const tool = measurementData.toolType || measurementData.toolName;
-
-  const displaySetInstanceUID = _getDisplaySetInstanceUID(
-    DisplaySetService,
-    SeriesInstanceUID,
-    SOPInstanceUID
-  );
-
-  const { handles, label } = measurementData;
-
-  const points = [];
-  Object.keys(handles).map(handle => {
-    if (['start', 'end'].includes(handle)) {
-      let point = {};
-      if (handles[handle].x) point.x = handles[handle].x;
-      if (handles[handle].y) point.y = handles[handle].y;
-      points.push(point);
-    }
-  });
-
-  return {
-    id: measurementData.id,
-    SOPInstanceUID: SOPInstanceUID,
-    FrameOfReferenceUID,
-    referenceSeriesUID: SeriesInstanceUID,
-    referenceStudyUID: StudyInstanceUID,
-    displaySetInstanceUID,
-    description: measurementData.description,
-    unit: measurementData.unit,
-    length: measurementData.length,
-    type: _getValueTypeFromToolType(tool),
-    points,
-    label,
-  };
-}
-
-function Bidirectional(
-  measurementData,
-  SOPInstanceUID,
-  FrameOfReferenceUID,
-  SeriesInstanceUID,
-  StudyInstanceUID,
-  DisplaySetService,
-  _getValueTypeFromToolType
-) {
-  const tool = measurementData.toolType || measurementData.toolName;
-
-  const displaySetInstanceUID = _getDisplaySetInstanceUID(
-    DisplaySetService,
-    SeriesInstanceUID,
-    SOPInstanceUID
-  );
-
-  const { handles, label } = measurementData;
-
-  const longAxis = [handles.start, handles.end];
-  const shortAxis = [handles.perpendicularStart, handles.perpendicularEnd];
-
-  return {
-    id: measurementData.id,
-    SOPInstanceUID: SOPInstanceUID,
-    FrameOfReferenceUID,
-    referenceSeriesUID: SeriesInstanceUID,
-    referenceStudyUID: StudyInstanceUID,
-    displaySetInstanceUID,
-    description: measurementData.description,
-    unit: measurementData.unit,
-    shortestDiameter: measurementData.shortestDiameter,
-    longestDiameter: measurementData.longestDiameter,
-    type: _getValueTypeFromToolType(tool),
-    points: { longAxis, shortAxis },
-    label,
-  };
-}
-
-function EllipticalRoi(
-  measurementData,
-  SOPInstanceUID,
-  FrameOfReferenceUID,
-  SeriesInstanceUID,
-  StudyInstanceUID,
-  DisplaySetService,
-  _getValueTypeFromToolType
-) {
-  const tool = measurementData.toolType || measurementData.toolName;
-
-  const displaySetInstanceUID = _getDisplaySetInstanceUID(
-    DisplaySetService,
-    SeriesInstanceUID,
-    SOPInstanceUID
-  );
-  const { handles, label } = measurementData;
-  const { start, end } = handles;
-
-  const halfXLength = Math.abs(start.x - end.x) / 2;
-  const halfYLength = Math.abs(start.y - end.y) / 2;
-
-  const points = [];
-  const center = { x: (start.x + end.x) / 2, y: (start.y + end.y) / 2 };
-
-  // To store similar to SR.
-  if (halfXLength > halfYLength) {
-    // X-axis major
-    // Major axis
-    points.push({ x: center.x - halfXLength, y: center.y });
-    points.push({ x: center.x + halfXLength, y: center.y });
-    // Minor axis
-    points.push({ x: center.x, y: center.y - halfYLength });
-    points.push({ x: center.x, y: center.y + halfYLength });
-  } else {
-    // Y-axis major
-    // Major axis
-    points.push({ x: center.x, y: center.y - halfYLength });
-    points.push({ x: center.x, y: center.y + halfYLength });
-    // Minor axis
-    points.push({ x: center.x - halfXLength, y: center.y });
-    points.push({ x: center.x + halfXLength, y: center.y });
-  }
-
-  return {
-    id: measurementData.id,
-    SOPInstanceUID: SOPInstanceUID,
-    FrameOfReferenceUID,
-    referenceSeriesUID: SeriesInstanceUID,
-    referenceStudyUID: StudyInstanceUID,
-    displaySetInstanceUID,
-    description: measurementData.description,
-    unit: measurementData.unit,
-    area:
-      measurementData.cachedStats &&
-      measurementData.cachedStats
-        .area /* TODO: Add concept names instead (descriptor) */,
-    type: _getValueTypeFromToolType(tool),
-    points,
-    label,
-  };
-}
-
-function ArrowAnnotate(
-  measurementData,
-  SOPInstanceUID,
-  FrameOfReferenceUID,
-  SeriesInstanceUID,
-  StudyInstanceUID,
-  DisplaySetService,
-  _getValueTypeFromToolType
-) {
-  const tool = measurementData.toolType || measurementData.toolName;
-
-  const displaySetInstanceUID = _getDisplaySetInstanceUID(
-    DisplaySetService,
-    SeriesInstanceUID,
-    SOPInstanceUID
-  );
-
-  const { handles } = measurementData;
-
-  const points = [];
-  Object.keys(handles).map(handle => {
-    if (['start', 'end'].includes(handle)) {
-      let point = {};
-      if (handles[handle].x) point.x = handles[handle].x;
-      if (handles[handle].y) point.y = handles[handle].y;
-      points.push(point);
-    }
-  });
-
-  return {
-    id: measurementData.id,
-    SOPInstanceUID: SOPInstanceUID,
-    FrameOfReferenceUID,
-    referenceSeriesUID: SeriesInstanceUID,
-    referenceStudyUID: StudyInstanceUID,
-    displaySetInstanceUID,
-    label: measurementData.text,
-    description: measurementData.description,
-    unit: measurementData.unit,
-    text: measurementData.text,
-    type: _getValueTypeFromToolType(tool),
-    points,
-  };
-}
-
-function _getDisplaySetInstanceUID(
-  DisplaySetService,
-  SeriesInstanceUID,
-  SOPInstanceUID
-) {
-  const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
-    SOPInstanceUID,
-    SeriesInstanceUID
-  );
-
-  return displaySet.displaySetInstanceUID;
-}
@@ -2,4 +2,4 @@ export {
  TrackedMeasurementsContext,
  TrackedMeasurementsContextProvider,
  useTrackedMeasurements,
-} from './TrackedMeasurementsContext.jsx';
+} from './TrackedMeasurementsContext.tsx';
@@ -44,7 +44,7 @@ const machineConfiguration = {
          target: 'promptHydrateStructuredReport',
          cond: 'hasNotIgnoredSRSeriesForHydration',
        },
-        RESTORE_PROMPT_HYDRATE_SR: 'promptHydrateStructuredReport'
+        RESTORE_PROMPT_HYDRATE_SR: 'promptHydrateStructuredReport',
      },
    },
    promptBeginTracking: {
@@ -224,7 +224,7 @@ const machineConfiguration = {
          {
            target: 'idle',
            actions: ['ignoreHydrationForSRSeries'],
-            cond: 'shouldIgnoreHydrationForSR'
+            cond: 'shouldIgnoreHydrationForSR',
          },
        ],
        onError: {
@@ -308,7 +308,10 @@ const defaultOptions = {
      ignoredSeries: [...ctx.ignoredSeries, evt.data.SeriesInstanceUID],
    })),
    ignoreHydrationForSRSeries: assign((ctx, evt) => ({
-      ignoredSRSeriesForHydration: [...ctx.ignoredSRSeriesForHydration, evt.data.srSeriesInstanceUID],
+      ignoredSRSeriesForHydration: [
+        ...ctx.ignoredSRSeriesForHydration,
+        evt.data.srSeriesInstanceUID,
+      ],
    })),
    addTrackedSeries: assign((ctx, evt) => ({
      prevTrackedSeries: [...ctx.trackedSeries],
@@ -376,7 +379,7 @@ const defaultOptions = {
      ctx.trackedSeries.length > 1 ||
      !ctx.trackedSeries.includes(evt.SeriesInstanceUID),
    hasNotIgnoredSRSeriesForHydration: (ctx, evt) => {
-      return !ctx.ignoredSRSeriesForHydration.includes(evt.SeriesInstanceUID)
+      return !ctx.ignoredSRSeriesForHydration.includes(evt.SeriesInstanceUID);
    },
    isNewStudy: (ctx, evt) =>
      !ctx.ignoredSeries.includes(evt.SeriesInstanceUID) &&
@@ -6,7 +6,7 @@ const RESPONSE = {
  SET_STUDY_AND_SERIES: 3,
 };

-function promptUser({ servicesManager, extensionManager }, ctx, evt) {
+function promptBeginTracking({ servicesManager, extensionManager }, ctx, evt) {
  const { UIViewportDialogService } = servicesManager.services;
  const { viewportIndex, StudyInstanceUID, SeriesInstanceUID } = evt;

@@ -33,7 +33,7 @@ function _askTrackMeasurements(UIViewportDialogService, viewportIndex) {
        id: 'prompt-begin-tracking-cancel',
        type: 'cancel',
        text: 'No',
-        value: RESPONSE.CANCEL
+        value: RESPONSE.CANCEL,
      },
      {
        id: 'prompt-begin-tracking-no-do-not-ask-again',
@@ -68,4 +68,4 @@ function _askTrackMeasurements(UIViewportDialogService, viewportIndex) {
  });
 }

-export default promptUser;
+export default promptBeginTracking;
@@ -10,10 +10,19 @@ const RESPONSE = {
  HYDRATE_REPORT: 5,
 };

-function promptUser({ servicesManager, extensionManager }, ctx, evt) {
-  const { UIViewportDialogService, DisplaySetService } = servicesManager.services;
+function promptHydrateStructuredReport(
+  { servicesManager, extensionManager },
+  ctx,
+  evt
+) {
+  const {
+    UIViewportDialogService,
+    DisplaySetService,
+  } = servicesManager.services;
  const { viewportIndex, displaySetInstanceUID } = evt;
-  const srDisplaySet = DisplaySetService.getDisplaySetByUID(displaySetInstanceUID)
+  const srDisplaySet = DisplaySetService.getDisplaySetByUID(
+    displaySetInstanceUID
+  );

  return new Promise(async function(resolve, reject) {
    const promptResult = await _askTrackMeasurements(
@@ -81,4 +90,4 @@ function _askTrackMeasurements(UIViewportDialogService, viewportIndex) {
  });
 }

-export default promptUser;
+export default promptHydrateStructuredReport;
@@ -1,9 +1,13 @@
-import createReportAsync from './../../_shared/createReportAsync.js';
+import createReportAsync from './../../_shared/createReportAsync';
 import createReportDialogPrompt from '../../_shared/createReportDialogPrompt';
 import getNextSRSeriesNumber from '../../_shared/getNextSRSeriesNumber';
 import RESPONSE from '../../_shared/PROMPT_RESPONSES';

-function promptUser({ servicesManager, extensionManager }, ctx, evt) {
+function promptSaveReport(
+  { servicesManager, commandsManager, extensionManager },
+  ctx,
+  evt
+) {
  const {
    UIDialogService,
    MeasurementService,
@@ -45,6 +49,7 @@ function promptUser({ servicesManager, extensionManager }, ctx, evt) {

      displaySetInstanceUIDs = await createReportAsync(
        servicesManager,
+        commandsManager,
        dataSource,
        trackedMeasurements,
        {
@@ -67,4 +72,4 @@ function promptUser({ servicesManager, extensionManager }, ctx, evt) {
  });
 }

-export default promptUser;
+export default promptSaveReport;
@@ -7,7 +7,7 @@ const RESPONSE = {
  NO_NOT_FOR_SERIES: 4,
 };

-function promptUser({ servicesManager, extensionManager }, ctx, evt) {
+function promptTrackNewSeries({ servicesManager, extensionManager }, ctx, evt) {
  const { UIViewportDialogService } = servicesManager.services;
  const { viewportIndex, StudyInstanceUID, SeriesInstanceUID } = evt;

@@ -105,4 +105,4 @@ function _askSaveDiscardOrCancel(UIViewportDialogService, viewportIndex) {
  });
 }

-export default promptUser;
+export default promptTrackNewSeries;
@@ -7,7 +7,7 @@ const RESPONSE = {
  NO_NOT_FOR_SERIES: 4,
 };

-function promptUser({ servicesManager, extensionManager }, ctx, evt) {
+function promptTrackNewStudy({ servicesManager, extensionManager }, ctx, evt) {
  const { UIViewportDialogService } = servicesManager.services;
  const { viewportIndex, StudyInstanceUID, SeriesInstanceUID } = evt;

@@ -104,4 +104,4 @@ function _askSaveDiscardOrCancel(UIViewportDialogService, viewportIndex) {
  });
 }

-export default promptUser;
+export default promptTrackNewStudy;